@Hunter Harms, I've worked in architecture offices doing everything from high rises to single apartments, and I've walked a few miles on job sites, so here's my opinion.
I have to reinforce much of what @Jeffrey Stasz was saying, but I also have a few tips on how to save cash while using a GC, with a few caveats. It depends on the size of your project and the types of people you're hiring, but I think his point of trusting your GC is huge. Find a good, reputable GC who is licensed, bonded, and insured and they will not do you wrong. A GC who is lic/bond/ins can lose their entire business and livelihood if they mess something up or are caught defrauding you, so start building your trust with that knowledge, and then find out more about their business and reputation. Ask to walk through previous jobs they've completed, ask to talk to previous clients, and work towards trust.
What you're describing is really what architects are hired to do, so look at it from that perspective. When we design big office towers we'll create a standards guidebook. Our client can use that guideline for future construction that might be done by a local design office. It might have everything from what font is used on signage to what carpet is used in the hallways, etc. What it also has is a spec book, which can be as vague or as specific as we want it to be (Jeff might laugh at that), and comes down to how much we trust our client's contractor to do a good job. The spec book specifies finish colors and products, but also has the details of what fasteners to use, what ASTM codes have to be followed, etc. Honestly, in residential construction we usually defer to the contractor on this stuff (even though we're the "pros"). They just know better.
All of that said, below I'll list method's I've used to save clients money in firms I've worked in, which maybe you can use as a model for your "systems". Keep in mind, you'll have to have a GC that understands how you want to work this system and who trusts you to coordinate this stuff. It's a HUGE pain in the *** for them if you get it wrong, so... something to keep in mind. Also this really only pertains to your jobs if you have high volume or a long working time for each project, which are two things that most flippers just don't have. I'll elaborate later.
1.) If you can get a trade discount (GC's, sometimes architects, tradesmen get it) buy your own finishes. The trade discount can save you 5 - 15% usually, plus GC markup for management.
2.) If you can get a trade discount buy your own appliances. Same as above.
3.) For finish work: hire your own subs, or do the work yourself. See Jeff's point about permitting for work. Depending on your jurisdiction, you may need to be lic/bond/ins just to lay a floor. You'll have to manage subs and inspect their work, or you'll have to get your hands dirty. Do you know what to inspect for and is your time worth those dollars? Those are the questions to ask yourself here.
With all of those points, besides a wealth of specialized knowledge, coordination is the biggest offering that a GC provides. If you order your own tile and it gets to the site on the wrong day, you're either in someone's way or slowing that project down and you're gonna pay for it. If you order a 24" wide range with 240V power and forgot to give your GC the cut sheet, you'll pay for that change order. If your GC already had the electrician install a 120V line and now he has to come back, every trade that follows him will have to come back too to redo the work he has to undo. Assumption of liability is the third thing that contractors offer that can actually save you money in the end.
If you are flipping dozens of houses a year, it might work to store thousands of sf of laminate floor and give your project manager the key to the warehouse. Likewise, if you are doing a high-end renovation and can foot the holding costs of a longer construction process, it might work to custom order all your materials per project and deal w/ scheduling coordination hiccups. Otherwise, I suggest it might be better to let your GC take the overhead cost.
You might find the best use of your efforts is to make a "soft" standards guide showing the palette you want, but allowing the GC some wiggle room. I.E. as long as it's gloss white 3x6 porcelain subway tile with dark grout, you don't care if they buy it from Laticrete or Mapei. Be as specific as you want, but be open to recommendations from your GC - maybe they can get you a discount on fireclay tile instead of porcelain, or they think an epoxy grout will be more durable than a sanded, or whatever.
Of course, if you're just painting and gluing down floor, and you know a good electrician to put in a couple of new outlets, do it yourself as long as your permitting office allows.
